I know this is a longshot, but its been known to happen especially on 6cyl Fords. Give you headers a good lookover. They could have hairline cracks that cause an exhaust leak that makes a ticking or tapping noise. Sometimes even shop mechanics have trouble finding this. This problem is common to mid-90s V6 Fords with cast iron manifolds. BTW if it is your tranny have it rebuilt with a reputable shop i.e. AAMCO or even a rebuilt motorcraft unit from your local Ford Dealer (I know: $$$$, but they are great!) or maybe you want a high performance AODE from Lentech, etc ($$$$ too) whatever works for you. I highly suggest an external tranny cooler (Ford Racing Cooler kit M-7077-D46 fits and works great). :thumbsup
P.S. Have you changed your ATF fluid? Sometimes a lot of problems are cured with a simple fluid and filter change. Be sure to use the correct Mercon.